AMBER Archive (2008)Subject: RE: AMBER: Electrostatic Energy Components
From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Nov 21 2008  18:12:44 CST
Dear Ross,
> Note, however that I have seen many times where people try to fit their own
> parameters and they produce a nice QM dihedral profile and then just fit the
> dihedral term to this (forgetting all about including the 14 EEL and VDW
> terms as well). Hence what they actually think they have fitted to they have
> not and when they then include it in a large simulation they don't realize
> that their actual force field parameters are bogus since they forgot the 14
> contributions.
Thanks for your explanations, but I could not understand this paragraph
of yours. Let's say we have created a nice QM profile of a particular
torsion. To do the fitting, the MM energy without the dihedral energy of
this particular torsion should be calculated (let's call it MM_1). This
means that an frcmod file with zero torsional barrier of the particular
torsion needs to be used. Then, QMMM_1 is calculated, which is fitted to
the desired cosine terms. If the fitting will include 2 cosine terms, for
example, QMMM_1 should be fitted to V_1 * (1+cos(n1*x)) + V_2 *
(1+cos(n2*x)).
In the whole above process, the 14EEL and VDW terms are not
used/calculated explicitly. They are included in the MM_1
energy implicitly. Did you mean that? Thanks.
Best regards,

Ilyas Yildirim, Ph.D.

= Hutchison Hall B#10  Department of Chemistry =
=  University of Rochester =
= 5852756766 (office)  =
= http://www.pas.rochester.edu/~yildirim/ =


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